The files in this directory were supplied by Haiming Wang and
Jessica Kissinger at University of Georgia's Center for Tropical &
Emerging Global Diseases & Department of Genetics. There are
two components:
1. A GUSdb adaptor (DAS::GUS) based on Bio::DB::Das::Chado in this
distribution. This adaptor is written to be reasonably generic, and
so it may be possible to use this as a template for creating an
adaptor for any database.
2. A sample configuration file (plasmodb.conf) that is similar to what
drives the synteny tracks in the gbrowse installation at
http://www.plasmodb.org/. For an example of what the display looks like,
see http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?start=101357;stop=121356;ref=MAL12;width=800;version=100;label=AnnotatedGenes-SyntenySpansVivaxMC-SyntenyGenesVivaxMC
This synteny view can use any GBrowse data adaptor, including the
Bio::DB::GFF and memory adaptors. Note that SynView requires
Tie::IxHash.
An example dataset is also included in the MAL11 directory; this directory
contains a GFF3 file, fasta file and a GBrowse configuration file set
up to use the memory adaptor.
This of course is a very brief introduction to SynView, for more
information, please see http://www.apidb.org/apps/SynView/, contact
Jessica or Haiming, or see their paper in Bioinformatics:
Wang, H., Su, Y., Mackey, A., Kraemer, E., and *Kissinger, J.C.* (2006)
SynView: A GBrowse-compatible Approach to Visualizing Comparative Genome
Data. Bioinformatics 22(18), 2308-2309
Thanks,
Scott Cain
cain@cshl.edu
November 6, 2006